Advertisement

Biophysical Reviews

, Volume 10, Issue 2, pp 631–640 | Cite as

The versatile mutational “repertoire” of Escherichia coli GroEL, a multidomain chaperonin nanomachine

  • Tomohiro Mizobata
  • Yasushi Kawata
Review

Abstract

The bacterial chaperonins are highly sophisticated molecular nanomachines, controlled by the hydrolysis of ATP to dynamically trap and remove from the environment unstable protein molecules that are susceptible to denaturation and aggregation. Chaperonins also act to assist in the refolding of these unstable proteins, providing a means by which these proteins may return in active form to the complex environment of the cell. The Escherichia coli GroE chaperonin system is one of the largest protein supramolecular complexes known, whose quaternary structure is required for segregating aggregation-prone proteins. Over the course of more than two decades of research on GroE, it has become accepted that GroE, more specifically the GroEL subunit, is a “high-tolerance” molecular system, capable of accommodating numerous mutations, while retaining its molecular integrity. In some cases, a given site of mutation was revealed to be absolutely required for GroEL function, providing hints regarding the network of signals and triggers that propel this unique system. In other instances, however, a mutation has produced a more delicate response, altering only part of, or in some cases, only a single facet of, the molecular mechanism, and these mutants have often provided invaluable hints on the extent of the complexity underlying chaperonin-assisted protein folding. In this review, we highlight some examples of the latter type of GroEL mutants which compose the unique “mutational repertoire” of GroEL and touch upon the important clues that each mutant provided to the overall effort to elucidate the details of GroE action.

Keywords

Chaperonin GroEL Molecular nanomachine Versatile mutation 

Notes

Funding

Portions of the manuscript performed by the authors was funded by a Grant-in-Aid for Scientific Research (C) (no. 22570119 to T. M.) from the Japan Society for the Promotion of Science (JSPS) and by the Strategic Research Program for Brain Sciences from the Japan Agency for Medical Research and Development (AMED).

Compliance with ethical standards

Conflict of interest

Tomohiro Mizobata declares that he has no conflict of interest. Yasushi Kawata declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

References

  1. Aharoni A, Horovitz A (1996) Inter-ring communication is disrupted in the GroEL mutant Arg13 → Gly; Ala126 → Val with known crystal structure. J Mol Biol 258:732–735.  https://doi.org/10.1006/jmbi.1996.0282 CrossRefPubMedGoogle Scholar
  2. Altamirano MM, Golbik R, Zahn R, Buckle AM, Fersht AR (1997) Refolding chromatography with immobilized mini-chaperones. Proc Natl Acad Sci U S A 94:3576–3578CrossRefPubMedPubMedCentralGoogle Scholar
  3. Altamirano MM, García C, Possani LD, Fersht AR (1999) Oxidative refolding chromatography: folding of the scorpion toxin Cn5. Nat Biotechnol 17:187–191.  https://doi.org/10.1038/6192 CrossRefPubMedGoogle Scholar
  4. Braig K, Otwinowski Z, Hegde R, Boisvert DC, Joachimiak A, Horwich AL, Sigler PB (1994) The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature 371:578–586CrossRefPubMedGoogle Scholar
  5. Chatellier J, Hill F, Lund PA, Fersht AR (1998) In vivo activities of GroEL minichaperones. Proc Natl Acad Sci U S A 95:9861–9866CrossRefPubMedPubMedCentralGoogle Scholar
  6. Chaudhry C, Horwich AL, Brunger AT, Adams PD (2004) Exploring the structural dynamics of the E. coli chaperonin GroEL using translation–libration–screw crystallographic refinement of intermediate states. J Mol Biol 342:229–245CrossRefPubMedGoogle Scholar
  7. Clare DK, Vasishtan D, Stagg S, Quispe J, Farr GW, Topf M, Horwich AL, Saibil HR (2012) ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin. Cell 149:113–123.  https://doi.org/10.1016/j.cell.2012.02.047 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Danziger O, Rivenzon-Segal D, Wolf SG, Horovitz A (2003) Conversion of the allosteric transition of GroEL from concerted to sequential by the single mutation Asp-155 → Ala. Proc Natl Acad Sci U S A 100:13797–13802.  https://doi.org/10.1073/pnas.2333925100 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Elad N, Farr GW, Clare DK, Orlova EV, Horwich AL, Saibil HR (2007) Topologies of a substrate protein bound to the chaperonin GroEL. Mol Cell 26:415–426CrossRefPubMedPubMedCentralGoogle Scholar
  10. Farr GW, Furtak K, Rowland MB, Ranson NA, Saibil HR, Kirchhausen T, Horwich AL (2000) Multivalent binding of nonnative substrate proteins by the chaperonin GroEL. Cell 100:561–573CrossRefPubMedGoogle Scholar
  11. Fenton WA, Kashi Y, Furtak K, Horwich AL (1994) Residues in chaperonin GroEL required for polypeptide binding and release. Nature 371:614–619CrossRefPubMedGoogle Scholar
  12. Fukui N, Araki K, Hongo K, Mizobata T, Kawata Y (2016) Modulating the effects of the bacterial chaperonin GroEL on fibrillogenic polypeptides through modification of domain hinge architecture. J Biol Chem 291:25217–25226.  https://doi.org/10.1074/jbc.M116.751925 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Georgopoulos CP, Hendrix RW, Kaiser AD, Wood WB (1972) Role of the host cell in bacteriophage morphogenesis: effects of a bacterial mutation on T4 head assembly. Nat New Biol 239:38–41CrossRefPubMedGoogle Scholar
  14. Gruber R, Horovitz A (2016) Allosteric mechanisms in chaperonin machines. Chem Rev 116:6588–6606.  https://doi.org/10.1021/acs.chemrev.5b00556 CrossRefPubMedGoogle Scholar
  15. Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475:324–332.  https://doi.org/10.1038/nature10317 CrossRefPubMedGoogle Scholar
  16. Hayer-Hartl M, Bracher A, Hartl FU (2016) The GroEL–GroES chaperonin machine: a nano-cage for protein folding. Trends Biochem Sci 41:62–76.  https://doi.org/10.1016/j.tibs.2015.07.009 CrossRefPubMedGoogle Scholar
  17. Heinemann U, Hahn M (1995) Circular permutation of polypeptide chains: implications for protein folding and stability. Prog Biophys Mol Biol 64:121–143CrossRefPubMedGoogle Scholar
  18. Iizuka R, Funatsu T (2016) Chaperonin GroEL uses asymmetric and symmetric reaction cycles in response to the concentration of non-native substrate proteins. Biophys Physicobiol 13:63–69.  https://doi.org/10.2142/biophysico.13.0_63 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Kawata Y, Kawagoe M, Hongo K, Miyazaki T, Higurashi T, Mizobata T, Nagai J (1999) Functional communications between the apical and equatorial domains of GroEL through the intermediate domain. Biochemistry 38:15731–15740CrossRefPubMedGoogle Scholar
  20. Kawe M, Plückthun A (2006) GroEL walks the fine line: the subtle balance of substrate and co-chaperonin binding by GroEL. A combinatorial investigation by design, selection and screening. J Mol Biol 357:411–426CrossRefPubMedGoogle Scholar
  21. Kim S, Willison KR, Horwich AL (1994) Cystosolic chaperonin subunits have a conserved ATPase domain but diverged polypeptide-binding domains. Trends Biochem Sci 19:543–548CrossRefPubMedGoogle Scholar
  22. Kim YE, Hipp MS, Bracher A, Hayer-Hartl M, Hartl FU (2013) Molecular chaperone functions in protein folding and proteostasis. Annu Rev Biochem 82:323–355.  https://doi.org/10.1146/annurev-biochem-060208-092442 CrossRefPubMedGoogle Scholar
  23. Machida K, Fujiwara R, Tanaka T, Sakane I, Hongo K, Mizobata T, Kawata Y (2009) Gly192 at hinge 2 site in the chaperonin GroEL plays a pivotal role in the dynamic apical domain movement that leads to GroES binding and efficient encapsulation of substrate proteins. Biochim Biophys Acta 1794:1344–1354.  https://doi.org/10.1016/j.bbapap.2008.12.003 CrossRefPubMedGoogle Scholar
  24. Martin J (1998) Role of the GroEL chaperonin intermediate domain in coupling ATP hydrolysis to polypeptide release. J Biol Chem 273:7351–7357CrossRefPubMedGoogle Scholar
  25. Mayhew M, da Silva AC, Martin J, Erdjument-Bromage H, Tempst P, Hartl FU (1996) Protein folding in the central cavity of the GroEL–GroES chaperonin complex. Nature 379:420–426CrossRefPubMedGoogle Scholar
  26. Miyazaki T, Yoshimi T, Furutsu Y, Hongo K, Mizobata T, Kanemori M, Kawata Y (2002) GroEL–substrate–GroES ternary complexes are an important transient intermediate of the chaperonin cycle. J Biol Chem 277:50621–50628.  https://doi.org/10.1074/jbc.M209183200 CrossRefPubMedGoogle Scholar
  27. Mizobata T, Uemura T, Isaji K, Hirayama T, Hongo K, Kawata Y (2011) Probing the functional mechanism of Escherichia coli GroEL using circular permutation. PLoS One 6:e26462.  https://doi.org/10.1371/journal.pone.0026462 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Mizuta T, Ando K, Uemura T, Kawata Y, Mizobata T (2013) Probing the dynamic process of encapsulation in Escherichia coli GroEL. PLoS One 8:e78135.  https://doi.org/10.1371/journal.pone.0078135 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Motojima F, Chaudhry C, Fenton WA, Farr GW, Horwich AL (2004) Substrate polypeptide presents a load on the apical domains of the chaperonin GroEL. Proc Natl Acad Sci U S A 101:15005–15012CrossRefPubMedPubMedCentralGoogle Scholar
  30. Ojha B, Fukui N, Hongo K, Mizobata T, Kawata Y (2016) Suppression of amyloid fibrils using the GroEL apical domain. Sci Rep 6:31041.  https://doi.org/10.1038/srep31041 CrossRefPubMedPubMedCentralGoogle Scholar
  31. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612.  https://doi.org/10.1002/jcc.20084 CrossRefPubMedGoogle Scholar
  32. Piggot TJ, Sessions RB, Burston SG (2012) Toward a detailed description of the pathways of allosteric communication in the GroEL chaperonin through atomistic simulation. Biochemistry 51:1707–1718.  https://doi.org/10.1021/bi201237a CrossRefPubMedGoogle Scholar
  33. Ranson NA, Clare DK, Farr GW, Houldershaw D, Horwich AL, Saibil HR (2006) Allosteric signaling of ATP hydrolysis in GroEL–GroES complexes. Nat Struct Mol Biol 13:147–152CrossRefPubMedPubMedCentralGoogle Scholar
  34. Rye HS, Burston SG, Fenton WA, Beechem JM, Xu Z, Sigler PB, Horwich AL (1997) Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL. Nature 388:792–798CrossRefPubMedGoogle Scholar
  35. Rye HS, Roseman AM, Chen S, Furtak K, Fenton WA, Saibil HR, Horwich AL (1999) GroEL–GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings. Cell 97:325–338CrossRefPubMedGoogle Scholar
  36. Saibil HR, Fenton WA, Clare DK, Horwich AL (2013) Structure and allostery of the chaperonin GroEL. J Mol Biol 425:1476–1487.  https://doi.org/10.1016/j.jmb.2012.11.028 CrossRefPubMedGoogle Scholar
  37. Sharapova OA, Yurkova MS, Fedorov AN (2016) A minichaperone-based fusion system for producing insoluble proteins in soluble stable forms. Protein Eng Des Sel 29:57–64.  https://doi.org/10.1093/protein/gzv060 CrossRefPubMedGoogle Scholar
  38. Takano T, Kakefuda T (1972) Involvement of a bacterial factor in morphogenesis of bacteriophage capsid. Nat New Biol 239:34–37CrossRefPubMedGoogle Scholar
  39. Viitanen PV, Lubben TH, Reed J, Goloubinoff P, O’Keefe DP, Lorimer GH (1990) Chaperonin-facilitated refolding of ribulose bisphosphate carboxylase and ATP hydrolysis by chaperonin 60 (groEL) are potassium dependent. Biochemistry 29:5665–5671CrossRefPubMedGoogle Scholar
  40. Wang Q, Buckle AM, Fersht AR (2000) Stabilization of GroEL minichaperones by core and surface mutations. J Mol Biol 298:917–926CrossRefPubMedGoogle Scholar
  41. Wang JD, Herman C, Tipton KA, Gross CA, Weissman JS (2002) Directed evolution of substrate-optimized GroEL/S chaperonins. Cell 111:1027–1039CrossRefPubMedGoogle Scholar
  42. Weissman JS, Hohl CM, Kovalenko O, Kashi Y, Chen S, Braig K, Saibil HR, Fenton WA, Horwich AL (1995) Mechanism of GroEL action: productive release of polypeptide from a sequestered position under GroES. Cell 83:577–587Google Scholar
  43. Weissman JS, Rye HS, Fenton WA, Beechem JM, Horwich AL (1996) Characterization of the active intermediate of a GroEL–GroES-mediated protein folding reaction. Cell 84:481–490CrossRefPubMedGoogle Scholar
  44. Williams TA, Fares MA (2010) The effect of chaperonin buffering on protein evolution. Genome Biol Evol 2:609–619.  https://doi.org/10.1093/gbe/evq045 CrossRefPubMedPubMedCentralGoogle Scholar
  45. Xu Z, Horwich AL, Sigler PB (1997) The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex. Nature 388:741–750CrossRefPubMedGoogle Scholar
  46. Yamamoto D, Ando T (2016) Chaperonin GroEL–GroES functions as both alternating and non-alternating engines. J Mol Biol 428:3090–3101.  https://doi.org/10.1016/j.jmb.2016.06.017 CrossRefPubMedGoogle Scholar
  47. Yébenes H, Mesa P, Muñoz IG, Montoya G, Valpuesta JM (2011) Chaperonins: two rings for folding. Trends Biochem Sci 36:424–432.  https://doi.org/10.1016/j.tibs.2011.05.003 CrossRefPubMedGoogle Scholar
  48. Yifrach O, Horovitz A (1994) Two lines of allosteric communication in the oligomeric chaperonin GroEL are revealed by the single mutation Arg196→Ala. J Mol Biol 243:397–401.  https://doi.org/10.1006/jmbi.1994.1667 CrossRefPubMedGoogle Scholar
  49. Yifrach O, Horovitz A (1995) Nested cooperativity in the ATPase activity of the oligomeric chaperonin GroEL. Biochemistry 34:5303–5308CrossRefPubMedGoogle Scholar
  50. Zahn R, Buckle AM, Perrett S, Johnson CM, Corrales FJ, Golbik R, Fersht AR (1996) Chaperone activity and structure of monomeric polypeptide binding domains of GroEL. Proc Natl Acad Sci U S A 93:15024–15029CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Graduate School of Engineering and Graduate School of Medical SciencesTottori UniversityTottoriJapan

Personalised recommendations